News
Reference sequence database for Bacteria and Archaea v1.4 released
2024-12-01
The database for reference protein sequences (bacteria and archaea) was updated. To update your reference sequence database run:
gapseq update-sequences -t Bacteria -Z latest # For Bacteria
gapseq update-sequences -t Archaea -Z latest # For Archaea
The sequences were retrieved from UniProt.
DOI of Zenodo data set: https://doi.org/10.5281/zenodo.16908828
Reference sequence database for Bacteria and Archaea v1.3 released
2024-11-06
The database for reference protein sequences (bacteria and archaea) was updated. gapseq should automatically download the latest version. The sequences were retrieved from UniProt Release 2024_05.
DOI of Zenodo data set: https://doi.org/10.5281/zenodo.14046824
gapseq version 1.4.0 now uses ‘cobrar’ instead of ‘sybil’
2024-10-25
Prior to v1.4.0, gapseq used the R packages ‘sybil’ and ‘sybilSBML’ for constraint-based metabolic modelling, including FBA and SBML file export. In addition, the R package ‘glpkAPI’ was required to interface with GLPK as an LP solver. All these dependencies are now replaced by the single R package ‘cobrar’.
What gapseq users need to know when updating from <=v1.3.1 to >=v1.4.0:
You will need to install ‘cobrar’ with the following commands:
install.packages("remotes") # only needed if 'remotes' is not installed yet
remotes::install_github("Waschina/cobrar")
Please make sure you have the system libraries ‘libSBML’ and ‘glpk’ installed before installing cobrar.
Detailed installation instructions for cobrar can be found in the cobrar documentation. There you will also find reference documentation and tutorials on how to use cobrar to analyse genome-scale metabolic network models, including those generated by gapseq.
Why this change? The ‘sybil’ family packages seem to be no longer regularly maintained, which has caused some compatibility issues with the libSBML system library and some installation problems.
An official release of a new version that uses ‘cobrar’ instead of ‘sybil’ will be made via github after a short testing phase of the latest development version.